The Ministry of Defence says there is "no evidence" that a multi-million-pound investigation took place into claims that the SAS had covered up war crimes.
Defence sources told the Mail on Sunday that a £6 million probe failed to find any evidence of wrongdoing.
The Royal Military Police reportedly began an investigation after being tipped off that SAS soldiers had altered official documents and used fake photographs to try to hide civilian deaths in Afghanistan. An MoD spokesman said, however:
"We are not aware of any evidence to support this allegation."
"As the Defence Secretary announced in February, the Royal Military Police expect to have discounted around 90% of allegations against our Armed Forces in Afghanistan by this summer.
"Our Armed Forces served in Afghanistan with great courage and professionalism.
"We hold our military to the highest standards. Where allegations are raised, it is right they are investigated."
According to the Mail on Sunday, however, sources said military police used a software programme to secretly monitor Special Forces troops while they used computers.
They were reportedly looking into claims that SAS soldiers had put pistols and rifles known to be used by the Taliban near dead civilians to make them look like enemy combatants.
However, no instances of the practice - known as 'drop weapons' - were revealed, according to the newspaper.
Former British Commander in Afghanistan, Colonel Richard Kemp, said:
"It is not their [the Royal Military Police's] job to waste vast sums of taxpayers' money to hound our bravest troops on the basis of flimsy allegations. The use of such extraordinary methods to bring down SAS soldiers, seemingly at any cost, smacks of a witch-hunt."
"Almost every household in Afghanistan has an arsenal of small arms, AK-47s and the like. Why would Special Forces need to bring these weapons with them on their raids?
"The claim was highly implausible to begin with. The alarming thing is that such a significant RMP investigation would have needed to be approved at a high level of command. I wonder who wanted to target the SAS?"